* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘ratematrix’ ... ** this is package ‘ratematrix’ version ‘1.2.4’ ** package ‘ratematrix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.3.0-5) 14.3.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpiqgofD/R.INSTALL1d24a310080fb7/ratematrix/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c MultRegimeMCMC.cpp -o MultRegimeMCMC.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29, from MultRegimeMCMC.cpp:1: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’ 66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.") | ^ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’ 66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.") | ^ g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ratematrix.so MultRegimeMCMC.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpiqgofD/R.INSTALL1d24a310080fb7/ratematrix/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpiqgofD/R.INSTALL1d24a310080fb7/ratematrix/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpiqgofD/R.INSTALL1d24a310080fb7/ratematrix/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ratematrix/00new/ratematrix/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘ratematrix’ finding HTML links ... done anoles html centrarchidae html checkConvergence html computeESS html continueMCMC html estimateTimeMCMC html extractCorrelation html fastSimmap html getStartPointFromPosterior html likelihoodFunction html logAnalyzer html makePrior html mergePosterior html mergeSimmap html plotPrior html plotRatematrix html plotRootValue html print.ratematrix_multi_chain html print.ratematrix_multi_mcmc html print.ratematrix_prior_function html print.ratematrix_prior_sample html print.ratematrix_single_chain html print.ratematrix_single_mcmc html ratematrix html ratematrixJointMCMC html ratematrixMCMC html readMCMC html readMCMC_Mk html samplePrior html simRatematrix html testRatematrix html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ratematrix)